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  <title>Depiction Service Overview</title>
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  <h2>Annotated List of Services Provided by this Site</h2>

  All Avalon services provided can be used as GET or POST requests with identical parameter naming.
  However, since SMILES are much (&gt;95%) shorter than MOL files, POST is preferred for MOL file handling.
  Short MOL files (e.g. from query structures for color-coding) can reasonably be put on the URL but real structure MOL
  files need to be send via POST in order to avoid ULR size limits.
  <p/>
  Most examples on this page use SMILES for structure definition, which requires a de-novo placement of atoms unless
  the SMILES string has a list of atom coordinates appended. MOL files (sent through POST) can be used to define the source structure
  keeping the coordinates. MOL files can also be used to define a query structure and use it to place the corresponding match atoms.
  <p/>
  There is also a page to show the speed of rendering about 500 <a href="drugs_test.jsp?size=150">drugs</a> (as GIF images) as well as a demo
  of rendered <a href="peptides_test.jsp?size=220">peptides and other large public molecules</a> (as PNG).
  Drugs are identified by their INN and were listed in the <a href="https://chempedia.info/info/derwent_world_drug_index/">WDI</a> as well as the
  <a href="https://www.ebi.ac.uk/chembldb/">CHEMBL</a> database. The peptides also have an INN and a CAS Registry number.

  <h3>Interactive Use</h3>

  <table class="tableStyle" border="both" width="*">
    <tbody class="tableBodyStyle">

      <tr>
        <td class="nameColumnStyle">
          <a href="SmilesVisualizer.jsp">Interactive SMILES Visualizer</a>
        </td>
        <td colspan="3" class="descColumnStyle">
            This is a demo application used for exercising the service as a SMILES renderer.
            <p/>
           It displays a web page with an input box for a SMILES string which is being rendered into a large image as-you-type.
           The first dropdown selects which kinds of aminoacid shortcuts are to be used for rendering.
           With second one, the depicter can be tuned to abbreviate long aliphatic chains to their molecular formula.
           <p/>
           Clicking on the large picture opens an link to a MOL file with content type 'chemical/x-mdl-molfile'.
           The smaller picture allow copying its URL with right-click/Properties.
           <p/>
           The link 'Converted SMILES' returns the text version of the abbreviated structure which is generated
           in the process of depicting with short-cuts.
           <p/>
           SMILES that contain '&gt;' characters are rendered as reaction SMILES.
        </td>
      </tr>
    </tbody>
  </table>
  <p/>

  <h3>Use of URL File Name Component</h3>

  Although the Avalon services are most often used for rendering pictures of SMILES or MOL file formatted structures,
  there are also some fringe services (chemical sructure fingerprint calculation, SMILES to MOL file conversion,
  and short-cut perception) based on features of the Avalon toolkit.
  <p/>
  The type (and MIME type) of the returned result is determined by the extension of the file name component of the URL.
  Appart from convenience, this convention also helps certain browsers guessing the display method if the MIME type isn't used.
  The following table lists the available file name extensions and their use. (The service returns an XML coded health report if the path
  equals <a HREF="mol-renderer/health.xml">health.xml</a>.)
  <p/>
  <table class="tableStyle" border="both">
    <tbody class="tableBodyStyle">
        <tr>
            <th class="tableHeaderCellStyle" width="100px">File Name Example</th>
            <th class="tableHeaderCellStyle" width="*">Description</th>
        </tr>

        <tr><th colspan="2">Extensions returning image representations</th></tr>

        <tr>
            <th>test.png</th>
            <td class="descColumnStyle">
                PNG formatted image (MIME type 'image/png') of the structure defined by the URL or parameters.
                The PNG is rendered using the Java ImageIO library which produces compressed
                8-bit color table PNG images by default. This is a reasonable choice since 2D
                chemical structure images usually have very few distinct colors.
            </td>
        </tr>

        <tr>
            <th>test.gif</th>
            <td class="descColumnStyle">
                GIF formatted image (MIME type 'image/png') of the structure defined by the URL or parameters.
                The GIF is rendered using the Java ImageIO library which produces compressed
                8-bit color table GIF images. GIFs do not support transparency.
            </td>
        </tr>

        <tr>
            <th>test.plt</th>
            <td class="descColumnStyle">
                Returns a list of plotting meta commands (MIME type 'text/plain') of the structure to be rendered.
            </td>
        </tr>

        <tr>
            <th>test.b64</th>
            <td class="descColumnStyle">
                Returns a base64 coded version (MIME type 'text/plain') of the PNG showing the structure to be rendered.
            </td>
        </tr>

        <tr>
            <th>test.md5</th>
            <td class="descColumnStyle">
                Returns an MD5 hashcode (MIME type 'text/plain') of the structure picture, the last 500 of which the server
                caches under that name.<p/>
                This method is typically used to implement a two step JavaScript protocol to first post a MOL file receiving the MD5
                hash code and then constructing an &lt;img&gt; tag's src attribute for rendering the image.
            </td>
        </tr>

        <tr><th colspan="2">Extensions returning results of general Cheminformatics services</th></tr>

        <tr>
            <th>test.smi</th>
            <td class="descColumnStyle">
                Returns the SMILES representation (MIME type 'text/plain') of the structure entered as a MOL file.
            </td>
        </tr>

        <tr>
            <th>test.mol</th>
            <td class="descColumnStyle">
               Returns the MDL/Accelrys MOL file representation (MIME type 'chemical/x-mdl-molfile')
               of the structure entered as a SMILES string. The browser should use the registered helper application,
               e.g. ISISDraw or ChemDraw, to display the resulting data.
            </td>
        </tr>

        <tr>
            <th>test.hex</th>
            <td class="descColumnStyle">
                Returns the hex coded fingerprint (MIME type 'text/plain') of the given structure.
            </td>
        </tr>

        <tr>
            <th>test.bin</th>
            <td class="descColumnStyle">
                Returns the 0/1 coded fingerprint (MIME type 'text/plain') of the given structure.
            </td>
        </tr>

        <tr>
            <th>test.lst</th>
            <td class="descColumnStyle">
                Returns the list of fingerprint bit numbers (MIME type 'text/plain') of the given structure.
            </td>
        </tr>

    </tbody>
  </table>
  <p/>

  <h3>Available URL-GET or POST Parameters</h3>

  All service parameters can be used both as GET and as POST parameters. However, molfile parameters might usually be to large
  for the limited URL size current browsers/servers can handle, although the HTTP standard does not limit URL lengths.
  URLs longer that 2000 characters will not work in most popular browsers. Note also that the MTU (Maximum Transmission Unit)
  of Ethernet is 1500 bytes.  <p/>

  <table class="tableStyle" border="both">
    <tbody class="tableBodyStyle">
      <tr>
        <th class="tableHeaderCellStyle" width="10%"> Parameter </th>
        <th class="tableHeaderCellStyle" width="50%"> Description </th>
        <th class="tableHeaderCellStyle" width="*"> Example(s) </th>
      </tr>

      <tr> <th class="tableHeaderCellStyle" colspan="3"> Input structure parameters </th> </tr>

      <tr>
        <td class="codeCell"> smiles </td>
        <td class="descColumnStyle">
            <a href="http://de.wikipedia.org/wiki/SMILES">SMILES</a> of the molecule to be rendered.
        </td>
        <td class="contentColumnStyle"> <code>smiles=c1ccccc1CCN</code> </td>
      </tr>

      <tr>
        <td class="codeCell"> molfile </td>
        <td class="descColumnStyle">
	    Provides an MDL/Accelrys/Symyx <a href='http://en.wikipedia.org/wiki/Chemical_table_file'>MOL file</a>
	    format definition of the molecule to be processed/rendered. This parameter is usually
	    provided via POST, because it is 20-50 times longer than the equivalent SMILES (w/o coordinates), but it does contain information
	    on the position of the atoms.<p/>
	    MOL files are usually the primary source of structural information and can contain decorations not (yet) rendered
	    by the Avalon depicter.
        </td>
        <td class="contentColumnStyle">
<pre size="-1" style="border: solid 1px; background-color: white;">
Pyridine
  -ISIS-  06211114472D
This is a line to be used for comments
  6  6  0  0  0  0  0  0  0  0999 V2000
   -0.8764   -2.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8776   -2.8648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1628   -3.2777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5537   -2.8644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5508   -2.0338    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1646   -1.6247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  2  3  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
M  END
</pre>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> md5 </td>
        <td class="descColumnStyle">
	    An MD5 hash code computed from the PNG bytes of the molecules rendering with the given parameters.
	   It is used for the two-step JavaScript rendering of MOL files that do not fit into the URL to be used for an IMG tag.
        </td>
        <td class="contentColumnStyle">
	    <code>4fac549da897a6ba99179f55dd8ebc5</code> is the MD5 hash computed by the following URL snippet:<p/>
            <a href="mol-renderer/t.md5?smiles=c1ccccc1O&amp;width=100&amp;height=80&amp;t=true">
            <code>mol-renderer/t.md5?smiles=c1ccccc1O&amp;width=100&amp;height=80&amp;t=true</code></a>
        <br/>
        This <a href="mol-renderer/t.html?smiles=c1ccccc1O&amp;width=100&amp;height=80&amp;t=true">link</a> opens an HTML page using this feature.
        </td>
      </tr>

      <tr> <th class="tableHeaderCellStyle" colspan="3"> Parameters controlling atom placement and rendering </th> </tr>

      <tr>
        <td class="codeCell"> tplMOL </td>
        <td class="descColumnStyle">
	    Query MOL file used to rotate the matching molecule such that the matching atoms are best aligned with the corresponding
	    template atoms. The template may contain all query features also available for Avalon substructure queries, e.g. generic
	    bond types, atom type lists, substitution counts, ring/chain bond constraints, etc.
        </td>
        <td class="contentColumnStyle">
<pre size="-1" style="border: solid 1px; background-color: white;">
Query mol file illustrating generic any atoms and an atom list
  -ISIS-  03050313422D

 10  9  1  0  0  0  0  0  0  0999 V2000
   -0.1806   -1.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1818   -2.8023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5331   -3.2152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2495   -2.8019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2466   -1.9713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5313   -1.5622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5288   -0.7372    0.0000 A   0  0  0  0  0  0  0  0  0  0  0  0
    1.9646   -3.2132    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5329   -4.0402    0.0000 A   0  0  0  0  0  0  0  0  0  0  0  0
    3.0875   -1.1958    0.0000 L   0  0  0  0  0  0  0  0  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
  2  3  1  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  3  4  2  0  0  0  0
  3  9  1  0  0  0  0
  1  2  2  0  0  0  0
 10 F    2  35  53
M  ALS  10  2 F Br  I   
M  END
</pre>
            
        </td>
      </tr>

      <tr>
        <td class="codeCell"> scaffold </td>
        <td class="descColumnStyle">
	    (Extended) SMILES coded version of <code>tplMOL</code>, which takes precedence if both parameters are present.
	    The SMILES may contain aromatic bonds to be more useful for substructure matching.<p/>
	    Note: This is just a SMILES (with possibly aromatic bond orders). Use the tplMOL parameter to represent more sophisticated query features.
        </td>
        <td class="contentColumnStyle">
	    <code>scaffold=c1ccccc1</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> chains </td>
        <td class="descColumnStyle">
            Abbreviate longer n-alkyl chains with their formula to reduce rendering size.<p/>
            This feature can also be activated by setting <code>chains</code> in the <code>flags</code> parameter.
        </td>
        <td class="contentColumnStyle">
            <code>chains=true</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> flags </td>
        <td class="descColumnStyle">
	    List of shortcut perception flags.<p/>
	    <dl>
		<dt><code>chains</code></dt>
		 <dd>Abbreviate long aliphatic carbon chains and PEG substructures.</dd>
		<dt><code>aminoacids</code></dt>
		<dd>Abbreviate the 22 (incl. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976440/">Pyl, Sec,</a>
		    and both His tautomers) standard aminoacids (in D- and L-forms).</dd>
		<dt><code>protecting-groups</code></dt>
		 <dd>Abbreviate certain protecting groups.</dd>
		<dt><code>extended</code></dt>
		 <dd>Abbreviate an extended set of amino acids, e.g. homocysteine.</dd>
		<dt><code>non-standard</code></dt>
		 <dd>Abbreviate certain non-standard aminoacids, e.g. N-methylated ones.</dd>
		<dt><code>catch-all</code></dt>
		 <dd>Use a catch-all shortcut to cover non-natural alpha aminoacids.</dd>
	     </dl> 
        </td>
        <td class="contentColumnStyle">
	    <code>flags=chains,aminoacids</code>
        </td>
      </tr>

      <tr> <th class="tableHeaderCellStyle" colspan="3"> Drawing parameters </th> </tr>

      <tr>
        <td class="codeCell"> width, w </td>
        <td class="descColumnStyle">
            Width of the picture in pixels.
        </td>
        <td class="contentColumnStyle">
            default: <code>width=300</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> height, h </td>
        <td class="descColumnStyle">
            Height of the picture in pixels.
        </td>
        <td class="contentColumnStyle">
            default: <code>height=250</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> b </td>
        <td class="descColumnStyle">
	    Setting this to 'true' adds a single pixel border to the resulting picture.
        </td>
        <td class="contentColumnStyle">
	    <code>b=true</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> bg </td>
        <td class="descColumnStyle">
            Defines the background of the picture using a 6-digit hex color code.
        </td>
        <td class="contentColumnStyle">
	    Set the background to yellow: <code>bg=FFFF77</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> t </td>
        <td class="descColumnStyle">
            Generates a drawing with a transparent background.
        </td>
        <td class="contentColumnStyle">
	    <code>t=true</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> title </td>
        <td class="descColumnStyle">
            Puts a title string at the top center of the rendering.
        </td>
        <td class="contentColumnStyle">
	    <code>title=This+is+a+title</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> footer </td>
        <td class="descColumnStyle">
            Puts a footer string at the bottom of the rendering.
        </td>
        <td class="contentColumnStyle">
	    <code>footer=This+is+a+footer</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> colored </td>
        <td class="descColumnStyle">
            Use the tplMOL/scaffold to color code the matching part of the molecule.
        </td>
        <td class="contentColumnStyle">
	    <code>colored=true</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> cb </td>
        <td class="descColumnStyle">
            Provide emphesis to support reading by color-blind users. Colored lines are drawn with 1.5 times the usual width and colored text is rendered as italic.
        </td>
        <td class="contentColumnStyle">
	    <code>cb=true</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> tpl_coords </td>
        <td class="descColumnStyle">
	    Defines how the coordinates of the scaffold/tplMOL are to be used.<p/>
	    <code>rotate</code> means that the rendered structure is to be rotated to assume the best fit to the matching scaffold atoms.
	    <code>force</code> places the atoms that match the template at those atoms and renders the remaining atoms de-novo around them.
	    This can, however, yield distorted results e.g. if scaffold chain bonds match into rings.
        </td>
        <td class="contentColumnStyle">
	    <code>tpl_coords=force</code>
        </td>
      </tr>

      <tr> <th class="tableHeaderCellStyle" colspan="3"> Fingerprint related parameters </th> </tr>

      <tr>
        <td class="codeCell"> nbits </td>
        <td class="descColumnStyle">
            Number of bits into which the fingerprint features are to be hashed.
        </td>
        <td class="contentColumnStyle">
	    <code>nbits=512</code>
        </td>
      </tr>

      <tr>
        <td class="codeCell"> asquery </td>
        <td class="descColumnStyle">
	    If <code>asquery=true</code>, then fingerprinting is not preceeded by implicit hydrogen and substitution count perception, i.e. the
	    structure is treated as a query.
        </td>
        <td class="contentColumnStyle">
	    <code>asquery=true</code>
        </td>
      </tr>

<!--	Not yet implemented
      <tr>
        <td class="codeCell"> usefplabels </td>
        <td class="descColumnStyle">
            Description
        </td>
        <td class="contentColumnStyle">
            Example
        </td>
      </tr>
-->

      <tr>
        <td class="codeCell"> bits </td>
        <td class="descColumnStyle">
	    List of fingerprint bit numbers to be used for coloring the structure by atoms required to show those fingerprint bits.<p/>
	    Atoms/bonds needed to have the first bit number set are colored in red. The remaining important parts are colored in blue.
        </td>
        <td class="contentColumnStyle">
	    <code>nbits=65536&amp;bits=12610,5940</code>
        </td>
      </tr>

    </tbody>
  </table>

  <h3>Annotated Examples</h3>

  <table class="tableStyle" border="both">
    <tbody class="tableBodyStyle">
      <tr>
        <th class="tableHeaderCellStyle" width="40%"> Description </th>
        <th class="tableHeaderCellStyle" width="*"> Example </th>
      </tr>

      <tr>
        <td class="descColumnStyle">
            Everybodies favourite drug rendered 100 by 80 pixels from a SMILES using a transparent background.<p/>
            URL: <code>mol-renderer/t.png?smiles=CCO&amp;width=100&amp;height=80&amp;t=true</code>
        </td>
        <td class="contentColumnStyle">
            <img src='mol-renderer/t.png?smiles=CCO&amp;width=100&amp;height=80&amp;t=true'/>
        </td>
      </tr>

      <tr>
        <td class="descColumnStyle">
            Simple esterification reaction with reacting bonds and atoms rendered for color-blind users.<p/>
            URL: <code class="word-break">mol-renderer/t.png?smiles=%5BCH3%3A1%5D%5BCH2%3A2%5D%5BOH%3A7%5D.%5BCH3%3A4%5D%5BC%3A5%5D%3A(%3D%5BO%3A6%5D)O%3E%3E%5BCH3%3A1%5D%5BCH2%3A2%5D%5BO%3A7%5D%5BC%3A5%5D(%3D%5BO%3A6%5D)%5BCH3%3A4%5D&amp;cb=true&amp;width=200&amp;height=80&amp;t=true</code>
        </td>
        <td class="contentColumnStyle">
            <img src='mol-renderer/t.png?smiles=%5BCH3%3A1%5D%5BCH2%3A2%5D%5BOH%3A7%5D.%5BCH3%3A4%5D%5BC%3A5%5D%3A(%3D%5BO%3A6%5D)O%3E%3E%5BCH3%3A1%5D%5BCH2%3A2%5D%5BO%3A7%5D%5BC%3A5%5D(%3D%5BO%3A6%5D)%5BCH3%3A4%5D&amp;cb=true&amp;width=200&amp;height=80&amp;t=true'/>
        </td>
      </tr>

      <tr>
        <td class="descColumnStyle" valign="middle">
            Fingerprint eaxmples based on phenol:
            <img src='mol-renderer/t.png?smiles=c1ccccc1O&amp;width=125&amp;height=100&amp;b=true'/>
        </td>
        <td class="contentColumnStyle">
            Compute 512 bit wide structure fingerprint using 0/1 format: <br/>
            <code><a href="mol-renderer/t.bin?smiles=c1ccccc1O&amp;nbits=512&amp;asquery=false">
                   mol-renderer/t.bin?smiles=c1ccccc1O&amp;nbits=512&amp;asquery=false</a></code> <p/>
            Compute 65536 bit wide query fingerprint using list format: <br/>
            <code><a href="mol-renderer/t.lst?smiles=c1ccccc1O&amp;nbits=65536&amp;asquery=true">
                    mol-renderer/t.lst?smiles=c1ccccc1O&amp;nbits=65536&amp;asquery=true</a></code> <p/>
            Rendering of phenol coloring atoms required to set fingerprint bit 53,5598,11706, and 23391 in a 65536 bit wide FP. The 'cb' parameter is set to 'true' to make the match more visible for color-blind users: <br/>
            <img src='mol-renderer/t.png?smiles=c1ccccc1O&amp;footer=Bit+53&amp;width=125&amp;height=100&amp;nbits=65536&amp;bits=53&amp;b=true&amp;cb=true'/>
            <img src='mol-renderer/t.png?smiles=c1ccccc1O&amp;footer=Bit+5598&amp;width=125&amp;height=100&amp;nbits=65536&amp;bits=5598&amp;b=true&amp;cb=true'/>
            <img src='mol-renderer/t.png?smiles=c1ccccc1O&amp;footer=Bit+11706&amp;width=125&amp;height=100&amp;nbits=65536&amp;bits=11706&amp;b=true&amp;cb=true'/>
            <img src='mol-renderer/t.png?smiles=c1ccccc1O&amp;footer=Bit+23391&amp;width=125&amp;height=100&amp;nbits=65536&amp;bits=23391&amp;b=true&amp;cb=true'/>
        </td>
      </tr>

      <tr>
        <td class="descColumnStyle">
            SMILEY-Man as a 210 by 140 pixel image using a yellow background and a (black) border.<p/>
            URL: <code class="word-break">mol-renderer/test.png?smiles=C12(C)CCC1(C)OCC(%3dC3C(CCO)CCC(CCC%3dC)C(CCC%3dC)CCC3(CCO))CO2&amp;w=210&amp;h=140&amp;bg=FFFF77&amp;b=true</code>
        </td>
        <td class="contentColumnStyle">
            <img src='mol-renderer/test.png?smiles=C12(C)CCC1(C)OCC(%3dC3C(CCO)CCC(CCC%3dC)C(CCC%3dC)CCC3(CCO))CO2&amp;w=210&amp;h=140&amp;bg=FFFF77&amp;b=true'/>
        </td>
      </tr>

      <tr>
        <td class="descColumnStyle">
            Molecule (PIRTENIDINE) with chain short-cuts<p/>
            URL: <code>mol-renderer/t.png?smiles=CCCCCCCCN=C1C=CN(CCCCCCCC)C=C1&amp;width=200&amp;height=180&amp;chains=true</code>
        </td>
        <td class="contentColumnStyle">
            <img src='mol-renderer/t.png?smiles=CCCCCCCCN=C1C=CN(CCCCCCCC)C=C1&amp;width=200&amp;height=180&amp;chains=true&amp;b=true'/>
        </td>
      </tr>

      <tr>
        <td class="descColumnStyle">
            Molecule rendered with a template used for coloring and/or atom placement.<p/>
	    The form provides the molecule to be rendered as a SMILES and the template for coloring as
	    a MOL file in a &lt;textarea&gt; tag.
        </td>
        <td class="contentColumnStyle">

	    <h3>Plain Rendering</h3>
<div style="padding:5px;border:2px solid black;">
<form method="POST" action="mol-renderer/test.png?w=220&amp;h=180">
<b>CIAPILOME:></b><input name="smiles" size="60" value="CC(=O)NN1C=NC(=O)C(C#N)=C1"/><br/>
<input type="submit" value="Show Molecule">
</form>
</div>
<p/>

	    <h3>Rendering With Template</h3>
<div style="padding:5px;border:2px solid black;">
<form method="POST" action="mol-renderer/test.png?w=220&amp;h=180">
    <b>AMEDALIN: </b> <input name="smiles" size="60" value="CNCCCC3(C)C(=O)N(c1ccccc1)c2ccccc23"/><br/>
Color Template: <input name="colored" type="checkbox" value="true"/> <br/>
Use Color-Blind Option: <input name="cb" type="checkbox" value="true"/> <p/>
Template Coordinates:
<select name="tpl_coords">
    <option value="">Ignore Coordinates</option>
    <option value="rotate">Rotate/Flip Molecule</option>
    <option value="force">Force Template Coordinates</option>
</select>
    <p/>

<textarea name="tplMOL" rows="20" cols="60">Substructure of Voltaren
  -ISIS-  07211409062D

 16 17  0  0  0  0  0  0  0  0999 V2000
   -3.6098    2.0488    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9570    2.4219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2951    2.0488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6424    2.4219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6424    3.1764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2951    3.5577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9570    3.1764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2928    1.2890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6337    0.9110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6314    0.1512    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2604    2.4303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2553    3.1830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5560    3.1918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5611    2.4391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9011    3.5617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9112    2.0562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 11 12  2  0  0  0  0
  1  2  1  0  0  0  0
 13 14  1  0  0  0  0
  2  7  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
 11 16  1  0  0  0  0
 12 15  1  0  0  0  0
 15 13  2  0  0  0  0
 14 16  2  0  0  0  0
  1 11  1  0  0  0  0
M  END
</textarea><p/>

<input type="submit" value="Show Molecule">
</form>
Other Examples (Copy/Paste into SMILES text box above):
<table>
    <tr><td><b>OXCARBAZEPINE:</b></td><td>NC(=O)N3c1ccccc1CC(=O)c2ccccc23</td></tr>
    <tr><td><b>LUMIRACOXIB:</b></td><td>Cc2ccc(Nc1c(F)cccc1Cl)c(CC(O)=O)c2</td></tr>
</table>
</div>

        </td>
      </tr>

      <tr>
        <td class="descColumnStyle">
            Using a POST form to render a query MOL file.
        </td>
        <td class="contentColumnStyle">
<div style="padding:5px;border:2px solid black;">
<form method="POST" action="mol-renderer/test.png?b=true">
<h3>Query MOL File</h3>
Width: <input name="w" size="5" value="600"/> <br/>
Height: <input name="h" size="5" value="400"/> <br/>
<textarea name="molfile" rows="20" cols="60">Common fuses aromatic with atom type lists
  ChemDraw04071310002D

 13 13  6  0  0  0  0  0  0  0999 V2000
   -1.0811    0.4125    0.0000 N
   -1.0811   -0.4125    0.0000 C
   -0.3666   -0.8250    0.0000 N
    0.3479   -0.4125    0.0000 C
    0.3479    0.4125    0.0000 C
   -0.3666    0.8250    0.0000 C
   -1.7953   -0.8250    0.0000 N
    1.0623    0.8250    0.0000 L
    1.0623   -0.8250    0.0000 L
    1.2122    1.6500    0.0000 L
    1.2122   -1.6500    0.0000 L
    1.7953    0.2416    0.0000 L
    1.7953   -0.2416    0.0000 L
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
  2  7  1  0
  5  8  1  0
  4  9  1  0
  8 10  8  0  1
  9 11  8  0  1
  8 12  8  0  1
  9 13  8  0  1
  8 F    4   6   7   8  16
  9 F    4   6   7   8  16
 10 F    4   6   7   8  16
 11 F    4   6   7   8  16
 12 F    4   6   7   8  16
 13 F    4   6   7   8  16
M  ALS   8  4 F C   N   O   S
M  ALS   9  4 F C   N   O   S
M  ALS  10  4 F C   N   O   S
M  ALS  11  4 F C   N   O   S
M  ALS  12  4 F C   N   O   S
M  ALS  13  4 F C   N   O   S
M  END
</textarea><p/>

<input type="submit" value="Show Query Molecule">
</form>
</div>

        </td>
      </tr>

      <tr>
        <td class="descColumnStyle">
            Using a POST form to convert a MOL file to a SMILES. (R-group atoms and certain query features are also supported.)
        </td>
        <td class="contentColumnStyle">
<div style="padding:5px;border:2px solid black;">
<form method="POST" action="mol-renderer/test.smi">
<h3>MOL File To Be Converted</h3>
Width: <input name="w" size="5" value="600"/> <br/>
Height: <input name="h" size="5" value="400"/> <br/>
<textarea name="molfile" rows="20" cols="60">Common fuses aromatic with atom type lists
  -ISIS-  06291514322D

  8  8  0  0  0  0  0  0  0  0999 V2000
    0.8111   -4.5041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8099   -5.3315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5247   -5.7444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2412   -5.3310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2383   -4.5005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5229   -4.0914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9512   -4.0853    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
    1.5245   -6.5694    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
  4  5  1  0  0  0  0
  2  3  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
  1  2  2  0  0  0  0
  5  7  1  0  0  0  0
  3  4  2  0  0  0  0
  3  8  1  0  0  0  0
M  RGP  2   7   1   8   2
M  END</textarea><p/>

<input type="submit" value="Convert to SMILES">
</form>
</div>

        </td>
      </tr>

    </tbody>
  </table>

</body>
</html>
